1. 02/07/2006CS267 Lecture 71 CS 267 Sources of Parallelism and Locality in Simulation – Part 2 James Demmel www.cs.berkeley.edu/~demmel/cs267_Spr06

2. 02/07/06CS267 Lecture 72 Recap of Last Lecture 4 kinds of simulations Discrete Event Systems Particle Systems Ordinary Differential Equations (ODEs) Today: Partial Differential Equations (PDEs) Common problems: Load balancing Dynamically, if load changes significantly during run Statically – Graph Partitioning –Sparse Matrix Vector Multiply (SpMV) Linear Algebra Solving linear systems of equations, eigenvalue problems Sparse and dense matrices Fast Particle Methods Solving in O(n) instead of O(n 2 )

3. 02/07/2006CS267 Lecture 73 Partial Differential Equations PDEs

4. 02/07/06CS267 Lecture 74 Continuous Variables, Continuous Parameters Examples of such systems include Elliptic problems (steady state, global space dependence) Electrostatic or Gravitational Potential: Potential(position) Hyperbolic problems (time dependent, local space dependence): Sound waves: Pressure(position,time) Parabolic problems (time dependent, global space dependence) Heat flow: Temperature(position, time) Diffusion: Concentration(position, time) Many problems combine features of above Fluid flow: Velocity,Pressure,Density(position,time) Elasticity: Stress,Strain(position,time)

5. 02/07/06CS267 Lecture 75 Example: Deriving the Heat Equation 01 x x+h Consider a simple problem A bar of uniform material, insulated except at ends Let u(x,t) be the temperature at position x at time t Heat travels from x-h to x+h at rate proportional to: As h  0, we get the heat equation: d u(x,t) (u(x-h,t)-u(x,t))/h - (u(x,t)- u(x+h,t))/h dt h = C * d u(x,t) d 2 u(x,t) dt dx 2 = C * x-h

6. 02/07/06CS267 Lecture 76 Details of the Explicit Method for Heat Discretize time and space using explicit approach (forward Euler) to approximate time derivative: (u(x,t+  ) – u(x,t))/  = C (u(x-h,t) – 2*u(x,t) + u(x+h,t))/h 2 u(x,t+  ) = u(x,t)+ C*  /h 2 *(u(x-h,t) – 2*u(x,t) + u(x+h,t)) Let z = C*  /h 2 u(x,t+  ) = z* u(x-h,t) + (1-2z)*u(x,t) + z*u(x+h,t) Change variable x to j*h, t to i* , and u(x,t) to u[j,i] u[j,i+1]= z*u[j-1,i]+ (1-2*z)*u[j,i]+ z*u[j+1,i] d u(x,t) d 2 u(x,t) dt dx 2 = C *

7. 02/07/06CS267 Lecture 77 Explicit Solution of the Heat Equation Use finite differences with u[j,i] as the temperature at time t= i*  (i = 0,1,2,…) and position x = j*h (j=0,1,…,N=1/h) initial conditions on u[j,0] boundary conditions on u[0,i] and u[N,i] At each timestep i = 0,1,2,... This corresponds to matrix vector multiply by T (next slide) Combine nearest neighbors on grid i=5 i=4 i=3 i=2 i=1 i=0 u[0,0] u[1,0] u[2,0] u[3,0] u[4,0] u[5,0] For j=0 to N u[j,i+1]= z*u[j-1,i]+ (1-2*z)*u[j,i] + z*u[j+1,i] where z =C*  /h 2 i j

8. 02/07/06CS267 Lecture 78 Matrix View of Explicit Method for Heat u[j,i+1]= z*u[j-1,i]+ (1-2*z)*u[j,i] + z*u[j+1,i] u[ :, i+1] = T * u[ :, i] where T is tridiagonal: L called Laplacian (in 1D) For a 2D mesh (5 point stencil) the Laplacian is pentadiagonal More on the matrix/grid views later 1-2z z z Graph and “3 point stencil” T = = I – z*L, L = 2 -1 -1 2 -1 -1 2 1-2z z z 1-2z z z 1-2z

9. 02/07/06CS267 Lecture 79 Parallelism in Explicit Method for PDEs Sparse matrix vector multiply, via Graph Partitioning Partitioning the space (x) into p largest chunks good load balance (assuming large number of points relative to p) minimized communication (only p chunks) Generalizes to multiple dimensions. arbitrary graphs (= arbitrary sparse matrices). Explicit approach often used for hyperbolic equations Problem with explicit approach for heat (parabolic): numerical instability. solution blows up eventually if z = C  /h 2 >.5 need to make the time step  very small when h is small:  <.5*h 2 /C

10. 02/07/06CS267 Lecture 710 Instability in Solving the Heat Equation Explicitly

11. 02/07/06CS267 Lecture 711 Implicit Solution of the Heat Equation Discretize time and space using implicit approach (backward Euler) to approximate time derivative: (u(x,t+  ) – u(x,t))/dt = C*(u(x-h,t+  ) – 2*u(x,t+  ) + u(x+h, t+  ))/h 2 u(x,t) = u(x,t+  ) - C*  /h 2 *(u(x-h,t+  ) – 2*u(x,t+  ) + u(x+h,t+  )) Let z = C*  /h 2 and change variable t to i* , x to j*h and u(x,t) to u[j,i] (I + z *L)* u[:, i+1] = u[:,i] Where I is identity and L is Laplacian as before 2 -1 -1 2 -1 -1 2 L = d u(x,t) d 2 u(x,t) dt dx 2 = C *

12. 02/07/06CS267 Lecture 712 Implicit Solution of the Heat Equation The previous slide used Backwards Euler, but using the trapezoidal rule gives better numerical properties Backwards Euler: (I + z *L)* u[:, i+1] = u[:,i] This turns into solving the following equation: Again I is the identity matrix and L is: Other problems yield Poisson’s equation (Lx = b in 1D) (I + (z/2)*L) * u[:,i+1]= (I - (z/2)*L) *u[:,i] 2 -1 -1 2 -1 -1 2 L = 2 Graph and “stencil”

13. 02/07/06CS267 Lecture 713 Relation of Poisson to Gravity, Electrostatics Poisson equation arises in many problems E.g., force on particle at (x,y,z) due to particle at 0 is -(x,y,z)/r 3, where r = sqrt(x 2 + y 2 + z 2 ) Force is also gradient of potential V = -1/r = -(d/dx V, d/dy V, d/dz V) = -grad V V satisfies Poisson’s equation (try working this out!) d 2 V + d 2 V + d 2 V = 0 dx 2 dy 2 dz 2

14. 02/07/06CS267 Lecture 714 2D Implicit Method Similar to the 1D case, but the matrix L is now Multiplying by this matrix (as in the explicit case) is simply nearest neighbor computation on 2D grid. To solve this system, there are several techniques. 4 -1 -1 -1 4 -1 -1 -1 4 -1 -1 4 -1 -1 -1 -1 4 -1 -1 -1 -1 4 -1 -1 4 -1 -1 -1 4 -1 -1 -1 4 L = 4 Graph and “5 point stencil” 3D case is analogous (7 point stencil)

15. 02/07/06CS267 Lecture 715 Algorithms for 2D (3D) Poisson Equation (N vars) AlgorithmSerialPRAMMemory #Procs Dense LUN 3 NN 2 N 2 Band LUN 2 (N 7/3 )NN 3/2 (N 5/3 )N JacobiN 2 NNN Explicit Inv.N log NNN Conj.GradientsN 3/2 N 1/2 *log NNN Red/Black SORN 3/2 N 1/2 NN Sparse LUN 3/2 (N 2 ) N 1/2 N*log N(N 4/3 ) N FFTN*log Nlog NNN MultigridNlog 2 NNN Lower boundNlog NN PRAM is an idealized parallel model with zero cost communication Reference: James Demmel, Applied Numerical Linear Algebra, SIAM, 1997. 22 2

16. 02/07/06CS267 Lecture 716 Overview of Algorithms Sorted in two orders (roughly): from slowest to fastest on sequential machines. from most general (works on any matrix) to most specialized (works on matrices “like” T). Dense LU: Gaussian elimination; works on any N-by-N matrix. Band LU: Exploits the fact that T is nonzero only on sqrt(N) diagonals nearest main diagonal. Jacobi: Essentially does matrix-vector multiply by T in inner loop of iterative algorithm. Explicit Inverse: Assume we want to solve many systems with T, so we can precompute and store inv(T) “for free”, and just multiply by it (but still expensive). Conjugate Gradient: Uses matrix-vector multiplication, like Jacobi, but exploits mathematical properties of T that Jacobi does not. Red-Black SOR (successive over-relaxation): Variation of Jacobi that exploits yet different mathematical properties of T. Used in multigrid schemes. Sparse LU: Gaussian elimination exploiting particular zero structure of T. FFT (fast Fourier transform): Works only on matrices very like T. Multigrid: Also works on matrices like T, that come from elliptic PDEs. Lower Bound: Serial (time to print answer); parallel (time to combine N inputs). Details in class notes and www.cs.berkeley.edu/~demmel/ma221.

17. 02/07/06CS267 Lecture 717 Mflop/s Versus Run Time in Practice Problem: Iterative solver for a convection-diffusion problem; run on a 1024-CPU NCUBE-2. Reference: Shadid and Tuminaro, SIAM Parallel Processing Conference, March 1991. SolverFlopsCPU Time(s)Mflop/s Jacobi3.82x10 12 21241800 Gauss-Seidel1.21x10 12 8851365 Multigrid2.13x10 9 7 318 Which solver would you select?

18. 02/07/06CS267 Lecture 718 Summary of Approaches to Solving PDEs As with ODEs, either explicit or implicit approaches are possible Explicit, sparse matrix-vector multiplication Implicit, sparse matrix solve at each step Direct solvers are hard (more on this later) Iterative solves turn into sparse matrix-vector multiplication –Graph partitioning Grid and sparse matrix correspondence: Sparse matrix-vector multiplication is nearest neighbor “averaging” on the underlying mesh Not all nearest neighbor computations have the same efficiency Depends on the mesh structure (nonzero structure) and the number of Flops per point.

19. 02/07/06CS267 Lecture 719 Comments on practical meshes Regular 1D, 2D, 3D meshes Important as building blocks for more complicated meshes Practical meshes are often irregular Composite meshes, consisting of multiple “bent” regular meshes joined at edges Unstructured meshes, with arbitrary mesh points and connectivities Adaptive meshes, which change resolution during solution process to put computational effort where needed

20. 02/07/06CS267 Lecture 720 Parallelism in Regular meshes Computing a Stencil on a regular mesh need to communicate mesh points near boundary to neighboring processors. Often done with ghost regions Surface-to-volume ratio keeps communication down, but Still may be problematic in practice Implemented using “ghost” regions. Adds memory overhead

21. 02/07/06CS267 Lecture 721 Composite mesh from a mechanical structure

22. 02/07/06CS267 Lecture 722 Converting the mesh to a matrix

23. 02/07/06CS267 Lecture 723 Effects of Ordering Rows and Columns on Gaussian Elimination

24. 02/07/06CS267 Lecture 724 Irregular mesh: NASA Airfoil in 2D (direct solution)

25. 02/07/06CS267 Lecture 725 Irregular mesh: Tapered Tube (multigrid)

26. 02/07/06CS267 Lecture 726 Source of Unstructured Finite Element Mesh: Vertebra Source: M. Adams, H. Bayraktar, T. Keaveny, P. Papadopoulos, A. Gupta Study failure modes of trabecular Bone under stress

27. 02/07/06CS267 Lecture 727 Micro-Computed Tomography  CT @ 22  m resolution Mechanical Testing E,  yield,  ult, etc. Methods:  FE modeling (Gordon Bell Prize, 2004) 3D image 2.5 mm cube 44  m elements  FE mesh Source: Mark Adams, PPPL Up to 537M unknowns

28. 02/07/06CS267 Lecture 728 Adaptive Mesh Refinement (AMR) Adaptive mesh around an explosion Refinement done by calculating errors Parallelism Mostly between “patches,” dealt to processors for load balance May exploit some within a patch (SMP) Projects: Titanium (http://www.cs.berkeley.edu/projects/titanium)http://www.cs.berkeley.edu/projects/titanium Chombo (P. Colella, LBL), KeLP (S. Baden, UCSD), J. Bell, LBL

29. 02/07/06CS267 Lecture 729 Adaptive Mesh Shock waves in a gas dynamics using AMR (Adaptive Mesh Refinement) See: http://www.llnl.gov/CASC/SAMRAI/http://www.llnl.gov/CASC/SAMRAI/ fluid density

30. 02/07/06CS267 Lecture 730 Challenges of Irregular Meshes How to generate them in the first place Start from geometric description of object Triangle, a 2D mesh partitioner by Jonathan Shewchuk 3D harder! How to partition them ParMetis, a parallel graph partitioner How to design iterative solvers PETSc, a Portable Extensible Toolkit for Scientific Computing Prometheus, a multigrid solver for finite element problems on irregular meshes How to design direct solvers SuperLU, parallel sparse Gaussian elimination These are challenges to do sequentially, more so in parallel

31. 02/07/06CS267 Lecture 731 Summary – sources of parallelism and locality Current attempts to categorize main “kernels” dominating simulation codes “7 Dwarfs” (Phil Colella, LBNL) Structured grids including locally structured grids, as in AMR Unstructured grids Spectral methods (Fast Fourier Transform) Dense Linear Algebra Sparse Linear Algebra Both explicit (SpMV) and implicit (solving) Particle Methods Monte Carlo (easy!)

32. 02/07/2006CS267 Lecture 732 Extra Slides

33. 02/07/06CS267 Lecture 733 High-end simulation in the physical sciences = 7 numerical methods : 1.Structured Grids (including locally structured grids, e.g. AMR) 2.Unstructured Grids 3.Fast Fourier Transform 4.Dense Linear Algebra 5.Sparse Linear Algebra 6.Particles 7.Monte Carlo Well-defined targets from algorithmic, software, and architecture standpoint Phillip Colella’s “Seven dwarfs” Add 4 for embedded 8. Search/Sort 9. Finite State Machine 10. Filter 11. Combinational logic Then covers all 41 EEMBC benchmarks Revize 1 for SPEC 7. Monte Carlo => Easily parallel (to add ray tracing) Then covers 26 SPEC benchrmarks Slide from “Defining Software Requirements for Scientific Computing”, Phillip Colella, 2004

34. 02/07/06CS267 Lecture 734 Composite Mesh from a Mechanical Structure

35. 02/07/06CS267 Lecture 735 Converting the Mesh to a Matrix

36. 02/07/06CS267 Lecture 736 Effects of Reordering on Gaussian Elimination

37. 02/07/06CS267 Lecture 737 Irregular mesh: NASA Airfoil in 2D

38. 02/07/06CS267 Lecture 738 Irregular mesh: Tapered Tube (Multigrid)

39. 02/07/06CS267 Lecture 739 CS267 Final Projects Project proposal Teams of 3 students, typically across departments Interesting parallel application or system Conference-quality paper High performance is key: Understanding performance, tuning, scaling, etc. More important the difficulty of problem Leverage Projects in other classes (but discuss with me first) Research projects

40. 02/07/06CS267 Lecture 740 Project Ideas Applications Implement existing sequential or shared memory program on distributed memory Investigate SMP trade-offs (using only MPI versus MPI and thread based parallelism) Tools and Systems Effects of reordering on sparse matrix factoring and solves Numerical algorithms Improved solver for immersed boundary method Use of multiple vectors (blocked algorithms) in iterative solvers

41. 02/07/06CS267 Lecture 741 Project Ideas Novel computational platforms Exploiting hierarchy of SMP-clusters in benchmarks Computing aggregate operations on ad hoc networks (Culler) Push/explore limits of computing on “the grid” Performance under failures Detailed benchmarking and performance analysis, including identification of optimization opportunities Titanium UPC IBM SP (Blue Horizon)

42. 02/07/06CS267 Lecture 742 Terminology Term hyperbolic, parabolic, elliptic, come from special cases of the general form of a second order linear PDE a*d 2 u/dx + b*d 2 u/dxdy + c*d 2 u/dy 2 + d*du/dx + e*du/dy + f = 0 where y is time Analog to solutions of general quadratic equation a*x 2 + b*xy + c*y 2 + d*x + e*y + f Backup slide: currently hidden.